OpenMS  2.6.0
PrecursorCorrection.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg, Oliver Alka $
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34 //
35 
36 #pragma once
37 
41 
44 
46 
47 #include <fstream>
48 #include <iostream>
49 #include <string>
50 #include <algorithm>
51 
52 namespace OpenMS
53 {
64 class OPENMS_DLLAPI PrecursorCorrection
65 {
66  public:
67 
68  static const std::string csv_header;
69 
78  static void getPrecursors(const MSExperiment & exp,
79  std::vector<Precursor> & precursors,
80  std::vector<double> & precursors_rt,
81  std::vector<Size> & precursor_scan_index);
82 
83 
98  static void writeHist(const String& out_csv,
99  const std::vector<double> & delta_mzs,
100  const std::vector<double> & mzs,
101  const std::vector<double> & rts);
116  static std::set<Size> correctToNearestMS1Peak(MSExperiment & exp,
117  double mz_tolerance,
118  bool ppm,
119  std::vector<double> & delta_mzs,
120  std::vector<double> & mzs,
121  std::vector<double> & rts);
122 
137  static std::set<Size> correctToHighestIntensityMS1Peak(MSExperiment & exp,
138  double mz_tolerance,
139  bool ppm,
140  std::vector<double> & delta_mzs,
141  std::vector<double> & mzs,
142  std::vector<double> & rts);
143 
144 
168  static std::set<Size> correctToNearestFeature(const FeatureMap& features,
169  MSExperiment & exp,
170  double rt_tolerance_s = 0.0,
171  double mz_tolerance = 0.0,
172  bool ppm = true,
173  bool believe_charge = false,
174  bool keep_original = false,
175  bool all_matching_features = false,
176  int max_trace = 2,
177  int debug_level = 0);
178 
179  protected:
180 
192  static bool overlaps_(const Feature& feature,
193  const double rt,
194  const double pc_mz,
195  const double rt_tolerance);
196 
209  static bool compatible_(const Feature& feature,
210  double pc_mz,
211  double mz_tolerance,
212  Size max_trace_number = 2,
213  int debug_level = 0);
214 
215 };
216 }
OpenMS::String
A more convenient string class.
Definition: String.h:59
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Constants.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
FeatureMap.h
MathFunctions.h
Precursor.h
MSExperiment.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:97
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
StandardTypes.h
OpenMS::PrecursorCorrection
This class provides methods for precursor correction.
Definition: PrecursorCorrection.h:64
OpenMS::PrecursorCorrection::csv_header
static const std::string csv_header
Definition: PrecursorCorrection.h:68